1
|
Dortaj H, Amani AM, Tayebi L, Azarpira N, Ghasemi Toudeshkchouei M, Hassanpour-Dehnavi A, Karami N, Abbasi M, Najafian-Najafabadi A, Zarei Behjani Z, Vaez A. Droplet-based microfluidics: an efficient high-throughput portable system for cell encapsulation. J Microencapsul 2024; 41:479-501. [PMID: 39077800 DOI: 10.1080/02652048.2024.2382744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 07/17/2024] [Indexed: 07/31/2024]
Abstract
One of the goals of tissue engineering and regenerative medicine is restoring primary living tissue function by manufacturing a 3D microenvironment. One of the main challenges is protecting implanted non-autologous cells or tissues from the host immune system. Cell encapsulation has emerged as a promising technique for this purpose. It involves entrapping cells in biocompatible and semi-permeable microcarriers made from natural or synthetic polymers that regulate the release of cellular secretions. In recent years, droplet-based microfluidic systems have emerged as powerful tools for cell encapsulation in tissue engineering and regenerative medicine. These systems offer precise control over droplet size, composition, and functionality, allowing for creating of microenvironments that closely mimic native tissue. Droplet-based microfluidic systems have extensive applications in biotechnology, medical diagnosis, and drug discovery. This review summarises the recent developments in droplet-based microfluidic systems and cell encapsulation techniques, as well as their applications, advantages, and challenges in biology and medicine. The integration of these technologies has the potential to revolutionise tissue engineering and regenerative medicine by providing a precise and controlled microenvironment for cell growth and differentiation. By overcoming the immune system's challenges and enabling the release of cellular secretions, these technologies hold great promise for the future of regenerative medicine.
Collapse
Affiliation(s)
- Hengameh Dortaj
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Mohammad Amani
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Lobat Tayebi
- Marquette University School of Dentistry, Milwaukee, WI, USA
| | - Negar Azarpira
- Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Ashraf Hassanpour-Dehnavi
- Tissue Engineering Lab, Department of Anatomical Sciences, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Neda Karami
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Milad Abbasi
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Atefeh Najafian-Najafabadi
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zeinab Zarei Behjani
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ahmad Vaez
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Biotechnology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| |
Collapse
|
2
|
Heiniger M, Vanella R, Walsh-Korb Z, Nash MA. Functionalized Polysaccharides Improve Sensitivity of Tyramide/Peroxidase Proximity Labeling Assays through Electrostatic Interactions. ACS Biomater Sci Eng 2024. [PMID: 39121180 DOI: 10.1021/acsbiomaterials.4c00895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2024]
Abstract
High-throughput assays that efficiently link genotype and phenotype with high fidelity are key to successful enzyme engineering campaigns. Among these assays, the tyramide/peroxidase proximity labeling method converts the product of an enzymatic reaction of a surface expressed enzyme to a highly reactive fluorescent radical, which labels the cell surface. In this context, maintaining the proximity of the readout reagents to the cell surface is crucial to prevent crosstalk and ensure that short-lived radical species react before diffusing away. Here, we investigated improvements in tyramide/peroxidase proximity labeling for enzyme screening. We modified chitosan (Cs) chains with horseradish peroxidase (HRP) and evaluated the effects of these conjugates on the efficiency of proximity labeling reactions on yeast cells displaying d-amino acid oxidase. By tethering HRP to chitosan through different chemical approaches, we localized the auxiliary enzyme close to the cell surface and enhanced the sensitivity of tyramide-peroxidase labeling reactions. We found that immobilizing HRP onto chitosan through a 5 kDa PEG linker improved labeling sensitivity by over 3.5-fold for substrates processed with a low turnover rate (e.g., d-lysine), while the sensitivity of the labeling for high activity substrates (e.g., d-alanine) was enhanced by over 0.6-fold. Such improvements in labeling efficiency broaden the range of enzymes and conditions that can be studied and screened by tyramide/peroxidase proximity labeling.
Collapse
Affiliation(s)
- Malvina Heiniger
- Department of Chemistry, University of Basel, Mattenstrasse 22, Basel 4058, Switzerland
| | - Rosario Vanella
- Department of Chemistry, University of Basel, Mattenstrasse 22, Basel 4058, Switzerland
| | - Zarah Walsh-Korb
- Department of Chemistry, University of Basel, Mattenstrasse 22, Basel 4058, Switzerland
| | - Michael A Nash
- Department of Chemistry, University of Basel, Mattenstrasse 22, Basel 4058, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Klingelbergstrasse 48, Basel 4056, Switzerland
| |
Collapse
|
3
|
Liu J, Du H, Huang L, Xie W, Liu K, Zhang X, Chen S, Zhang Y, Li D, Pan H. AI-Powered Microfluidics: Shaping the Future of Phenotypic Drug Discovery. ACS APPLIED MATERIALS & INTERFACES 2024; 16:38832-38851. [PMID: 39016521 DOI: 10.1021/acsami.4c07665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Phenotypic drug discovery (PDD), which involves harnessing biological systems directly to uncover effective drugs, has undergone a resurgence in recent years. The rapid advancement of artificial intelligence (AI) over the past few years presents numerous opportunities for augmenting phenotypic drug screening on microfluidic platforms, leveraging its predictive capabilities, data analysis, efficient data processing, etc. Microfluidics coupled with AI is poised to revolutionize the landscape of phenotypic drug discovery. By integrating advanced microfluidic platforms with AI algorithms, researchers can rapidly screen large libraries of compounds, identify novel drug candidates, and elucidate complex biological pathways with unprecedented speed and efficiency. This review provides an overview of recent advances and challenges in AI-based microfluidics and their applications in drug discovery. We discuss the synergistic combination of microfluidic systems for high-throughput screening and AI-driven analysis for phenotype characterization, drug-target interactions, and predictive modeling. In addition, we highlight the potential of AI-powered microfluidics to achieve an automated drug screening system. Overall, AI-powered microfluidics represents a promising approach to shaping the future of phenotypic drug discovery by enabling rapid, cost-effective, and accurate identification of therapeutically relevant compounds.
Collapse
Affiliation(s)
- Junchi Liu
- Department of Anesthesiology, The First Hospital of Jilin University, 71 Xinmin Street, Changchun 130012, China
| | - Hanze Du
- Department of Endocrinology, Key Laboratory of Endocrinology of National Health Commission, Translation Medicine Centre, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Lei Huang
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, School and Hospital of Stomatology, Jilin University, 1500 Qinghua Road, Changchun 130012, China
| | - Wangni Xie
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, School and Hospital of Stomatology, Jilin University, 1500 Qinghua Road, Changchun 130012, China
| | - Kexuan Liu
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, School and Hospital of Stomatology, Jilin University, 1500 Qinghua Road, Changchun 130012, China
| | - Xue Zhang
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, School and Hospital of Stomatology, Jilin University, 1500 Qinghua Road, Changchun 130012, China
| | - Shi Chen
- Department of Endocrinology, Key Laboratory of Endocrinology of National Health Commission, Translation Medicine Centre, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Yuan Zhang
- Department of Anesthesiology, The First Hospital of Jilin University, 71 Xinmin Street, Changchun 130012, China
| | - Daowei Li
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, School and Hospital of Stomatology, Jilin University, 1500 Qinghua Road, Changchun 130012, China
| | - Hui Pan
- Department of Endocrinology, Key Laboratory of Endocrinology of National Health Commission, Translation Medicine Centre, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| |
Collapse
|
4
|
Laurent JM, Jain A, Kan A, Steinacher M, Enrriquez Casimiro N, Stavrakis S, deMello AJ, Studart AR. Directed evolution of material-producing microorganisms. Proc Natl Acad Sci U S A 2024; 121:e2403585121. [PMID: 39042685 PMCID: PMC11295069 DOI: 10.1073/pnas.2403585121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 06/20/2024] [Indexed: 07/25/2024] Open
Abstract
Nature is home to a variety of microorganisms that create materials under environmentally friendly conditions. While this offers an attractive approach for sustainable manufacturing, the production of materials by native microorganisms is usually slow and synthetic biology tools to engineer faster microorganisms are only available when prior knowledge of genotype-phenotype links is available. Here, we utilize a high-throughput directed evolution platform to enhance the fitness of whole microorganisms under selection pressure and identify genetic pathways to enhance the material production capabilities of native species. Using Komagataeibacter sucrofermentans as a model cellulose-producing microorganism, we show that our droplet-based microfluidic platform enables the directed evolution of these bacteria toward a small number of cellulose overproducers from an initial pool of 40,000 random mutants. Sequencing of the evolved strains reveals an unexpected link between the cellulose-forming ability of the bacteria and a gene encoding a protease complex responsible for protein turnover in the cell. The ability to enhance the fitness of microorganisms toward a specific phenotype and to unravel genotype-phenotype links makes this high-throughput directed evolution platform a promising tool for the development of new strains for the sustainable manufacturing of materials.
Collapse
Affiliation(s)
- Julie M. Laurent
- Department of Materials, Complex Materials, ETH Zürich, Zürich8093, Switzerland
| | - Ankit Jain
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zürich, Zürich8093, Switzerland
| | - Anton Kan
- Department of Materials, Complex Materials, ETH Zürich, Zürich8093, Switzerland
| | - Mathias Steinacher
- Department of Materials, Complex Materials, ETH Zürich, Zürich8093, Switzerland
| | | | - Stavros Stavrakis
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zürich, Zürich8093, Switzerland
| | - Andrew J. deMello
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zürich, Zürich8093, Switzerland
| | - André R. Studart
- Department of Materials, Complex Materials, ETH Zürich, Zürich8093, Switzerland
| |
Collapse
|
5
|
Waeterschoot J, Kayahan E, Breukers J, Lammertyn J, Casadevall I Solvas X. The effects of droplet stabilization by surfactants and nanoparticles on leakage, cross-talk, droplet stability, and cell adhesion. RSC Adv 2024; 14:24115-24129. [PMID: 39091374 PMCID: PMC11292313 DOI: 10.1039/d4ra04298k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 07/01/2024] [Indexed: 08/04/2024] Open
Abstract
Partially fluorinated nanoparticles (FNPs) have been proposed as a promising alternative for stabilising aqueous droplets in fluorinated oils. The exceptional energetic stability of FNPs at the droplet interface holds the potential for minimising leakage, enhancing stability, and promoting improved cell adhesion. However, their lower diffusion coefficient compared to surfactants presents challenges in achieving rapid droplet stabilisation, which is important in microfluidics applications. While several studies have focused on some of these aspects, a comprehensive study and direct comparison with conventional fluorosurfactants is still missing. In this manuscript, we undertake an examination and comparison of four crucial facets of both FNP- and surfactant-stabilised droplets: leakage of compounds, emulsion stability, droplet formation dynamics and cell adhesion. Contrary to what has previously been claimed, our findings demonstrate that FNPs only reduce leakage and cross-talk in very specific cases (e.g., resorufin), failing to provide enhanced compartmentalisation for highly hydrophobic dyes (e.g., rhodamine dyes). On the other hand, FNP-stabilised droplets indeed exhibit greater long-term stability compared to their surfactant-stabilised counterparts. Regarding the size of droplets generated via a diversity of microfluidic methods, no significant differences were observed between FNP-stabilised and surfactant-stabilised droplets. Finally, the previously reported improvements in cell adhesion and spreading on FNP-stabilised interfaces is limited to flat oil/water (o/w) interfaces and could not be observed within droplets. These comprehensive analyses shed light on the nuanced performance of FNPs and commercial fluorosurfactants as stabilising agents for aqueous droplets in fluorinated oils, contributing valuable insights for choosing the correct formulation for specific droplet-based microfluidics applications.
Collapse
Affiliation(s)
- Jorik Waeterschoot
- Biomimetics Group, Divison of Mechatronics, Biostatistics and Sensors (MeBios), Department of Biosystems KU Leuven, Willem de Croylaan 42 3001 Leuven Belgium
| | - Emine Kayahan
- Biomimetics Group, Divison of Mechatronics, Biostatistics and Sensors (MeBios), Department of Biosystems KU Leuven, Willem de Croylaan 42 3001 Leuven Belgium
| | - Jolien Breukers
- Biosensors Group, Divison of Mechatronics, Biostatistics and Sensors (MeBios), Department of Biosystems KU Leuven, Willem de Croylaan 42 3001 Heverlee Belgium
| | - Jeroen Lammertyn
- Biosensors Group, Divison of Mechatronics, Biostatistics and Sensors (MeBios), Department of Biosystems KU Leuven, Willem de Croylaan 42 3001 Heverlee Belgium
| | - Xavier Casadevall I Solvas
- Biomimetics Group, Divison of Mechatronics, Biostatistics and Sensors (MeBios), Department of Biosystems KU Leuven, Willem de Croylaan 42 3001 Leuven Belgium
| |
Collapse
|
6
|
Adams SK, Ducharme GE, Loveday EK. All the single cells: if you like it then you should put some virus on it. J Virol 2024; 98:e0127323. [PMID: 38904395 DOI: 10.1128/jvi.01273-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024] Open
Abstract
Across a rich 70-year history, single-cell virology has revealed the impact of host and pathogen heterogeneity during virus infections. Recent technological innovations have enabled higher-resolution analyses of cellular and viral heterogeneity. Furthermore, single-cell analysis has revealed extreme phenotypes and provided additional insights into host-pathogen dynamics. Using a single-cell approach to explore fundamental virology questions, contemporary researchers have contributed to a revival of interest in single-cell virology with increased insights and enthusiasm.
Collapse
Affiliation(s)
- Sophia K Adams
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
| | - Grace E Ducharme
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
| | - Emma K Loveday
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
| |
Collapse
|
7
|
Padhy P, Zaman MA, Jensen MA, Cheng YT, Huang Y, Wu M, Galambos L, Davis RW, Hesselink L. Dielectrophoretic bead-droplet reactor for solid-phase synthesis. Nat Commun 2024; 15:6159. [PMID: 39039069 PMCID: PMC11263596 DOI: 10.1038/s41467-024-49284-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 05/29/2024] [Indexed: 07/24/2024] Open
Abstract
Solid-phase synthesis underpins many advances in synthetic and combinatorial chemistry, biology, and material science. The immobilization of a reacting species on the solid support makes interfacing of reagents an important challenge in this approach. In traditional synthesis columns, this leads to reaction errors that limit the product yield and necessitates excess consumption of the mobile reagent phase. Although droplet microfluidics can mitigate these problems, its adoption is fundamentally limited by the inability to controllably interface microbeads and reagent droplets. Here, we introduce Dielectrophoretic Bead-Droplet Reactor as a physical method to implement solid-phase synthesis on individual functionalized microbeads by encapsulating and ejecting them from microdroplets by tuning the supply voltage. Proof-of-concept demonstration of the enzymatic coupling of fluorescently labeled nucleotides onto the bead using this reactor yielded a 3.2-fold higher fidelity over columns through precise interfacing of individual microreactors and beads. Our work combines microparticle manipulation and droplet microfluidics to address a long-standing problem in solid-phase synthesis with potentially wide-ranging implications.
Collapse
Affiliation(s)
- Punnag Padhy
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA.
| | - Mohammad Asif Zaman
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Michael Anthony Jensen
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA.
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA.
| | - Yao-Te Cheng
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Yogi Huang
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Mo Wu
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Ludwig Galambos
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Ronald Wayne Davis
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Lambertus Hesselink
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA.
| |
Collapse
|
8
|
Kasputis T, Yeh PC, Liu L, Marano J, Weger-Lucarelli J, Du K, Lin L, Chen J. Development of a self-powered digital LAMP microfluidic chip (SP-dChip) for the detection of emerging viruses. LAB ON A CHIP 2024; 24:3490-3497. [PMID: 38920004 PMCID: PMC11272487 DOI: 10.1039/d4lc00265b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
Point-of-care (POC) diagnostics have emerged as a crucial technology for emerging pathogen detections to enable rapid and on-site detection of infectious diseases. However, current POC devices often suffer from limited sensitivity with poor reliability to provide quantitative readouts. In this paper, we present a self-powered digital loop-mediated isothermal amplification (dLAMP) microfluidic chip (SP-dChip) for the rapid and quantitative detection of nucleic acids. The SP-dChip utilizes a vacuum lung design to passively digitize samples into individual nanoliter wells for high-throughput analysis. The superior digitization scheme is further combined with reverse transcription loop-mediated isothermal amplification (RT-LAMP) to demonstrate dLAMP detection of Zika virus (ZIKV). Firstly, the LAMP assay is loaded into the chip and passively digitized into individual wells. Mineral oil is then pipetted through the chip to differentiate each well as an individual reactor. The chip did not require any external pumping or power input for rapid and reliable results to detect ZIKA RNA as low as 100 copies per μL within one hour. As such, this SP-dChip offers a new class of solutions for truly affordable, portable, and quantitative POC detections for emerging viruses.
Collapse
Affiliation(s)
- Tom Kasputis
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Po-Chen Yeh
- Department of Mechanical Engineering, University of California, Berkeley, CA, USA
| | - Li Liu
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - Jeffrey Marano
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Blacksburg, VA, USA
- Department of Biomedical Science, Colorado State University, Fort Collins, CO, USA
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Blacksburg, VA, USA
| | - Ke Du
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - Liwei Lin
- Department of Mechanical Engineering, University of California, Berkeley, CA, USA
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA
- Department of Bioengineering, University of California, Riverside, CA, USA.
| |
Collapse
|
9
|
Saleski TE, Peng H, Lengger B, Wang J, Jensen MK, Jensen ED. High-throughput G protein-coupled receptor-based autocrine screening for secondary metabolite production in yeast. Biotechnol Bioeng 2024. [PMID: 38973176 DOI: 10.1002/bit.28797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/09/2024]
Abstract
Biosensors are valuable tools in accelerating the test phase of the design-build-test-learn cycle of cell factory development, as well as in bioprocess monitoring and control. G protein-coupled receptor (GPCR)-based biosensors enable cells to sense a wide array of molecules and environmental conditions in a specific manner. Due to the extracellular nature of their sensing, GPCR-based biosensors require compartmentalization of distinct genotypes when screening production levels of a strain library to ensure that detected levels originate exclusively from the strain under assessment. Here, we explore the integration of production and sensing modalities into a single Saccharomyces cerevisiae strain and compartmentalization using three different methods: (1) cultivation in microtiter plates, (2) spatial separation on agar plates, and (3) encapsulation in water-in-oil-in-water double emulsion droplets, combined with analysis and sorting via a fluorescence-activated cell sorting machine. Employing tryptamine and serotonin as proof-of-concept target molecules, we optimize biosensing conditions and demonstrate the ability of the autocrine screening method to enrich for high producers, showing the enrichment of a serotonin-producing strain over a nonproducing strain. These findings illustrate a workflow that can be adapted to screening for a wide range of complex chemistry at high throughput using commercially available microfluidic systems.
Collapse
Affiliation(s)
- Tatyana E Saleski
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Huadong Peng
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
| | - Bettina Lengger
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Jinglin Wang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Michael Krogh Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Emil D Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| |
Collapse
|
10
|
Schnettler JD, Wang MS, Gantz M, Bunzel HA, Karas C, Hollfelder F, Hecht MH. Selection of a promiscuous minimalist cAMP phosphodiesterase from a library of de novo designed proteins. Nat Chem 2024; 16:1200-1208. [PMID: 38702405 PMCID: PMC11230910 DOI: 10.1038/s41557-024-01490-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 02/27/2024] [Indexed: 05/06/2024]
Abstract
The ability of unevolved amino acid sequences to become biological catalysts was key to the emergence of life on Earth. However, billions of years of evolution separate complex modern enzymes from their simpler early ancestors. To probe how unevolved sequences can develop new functions, we use ultrahigh-throughput droplet microfluidics to screen for phosphoesterase activity amidst a library of more than one million sequences based on a de novo designed 4-helix bundle. Characterization of hits revealed that acquisition of function involved a large jump in sequence space enriching for truncations that removed >40% of the protein chain. Biophysical characterization of a catalytically active truncated protein revealed that it dimerizes into an α-helical structure, with the gain of function accompanied by increased structural dynamics. The identified phosphodiesterase is a manganese-dependent metalloenzyme that hydrolyses a range of phosphodiesters. It is most active towards cyclic AMP, with a rate acceleration of ~109 and a catalytic proficiency of >1014 M-1, comparable to larger enzymes shaped by billions of years of evolution.
Collapse
Affiliation(s)
| | - Michael S Wang
- Department of Chemistry, Princeton University, Princeton, USA
| | - Maximilian Gantz
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - H Adrian Bunzel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Christina Karas
- Department of Molecular Biology, Princeton University, Princeton, USA
| | | | - Michael H Hecht
- Department of Chemistry, Princeton University, Princeton, USA.
| |
Collapse
|
11
|
Sharkey C, White R, Finocchiaro M, Thomas J, Estevam J, Konry T. Advancing Point-of-Care Applications with Droplet Microfluidics: From Single-Cell to Multicellular Analysis. Annu Rev Biomed Eng 2024; 26:119-139. [PMID: 38316063 DOI: 10.1146/annurev-bioeng-110222-102142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Recent advances in single-cell and multicellular microfluidics technology have provided powerful tools for studying cancer biology and immunology. The ability to create controlled microenvironments, perform high-throughput screenings, and monitor cellular interactions at the single-cell level has significantly advanced our understanding of tumor biology and immune responses. We discuss cutting-edge multicellular and single-cell microfluidic technologies and methodologies utilized to investigate cancer-immune cell interactions and assess the effectiveness of immunotherapies. We explore the advantages and limitations of the wide range of 3D spheroid and single-cell microfluidic models recently developed, highlighting the various approaches in device generation and applications in immunotherapy screening for potential opportunities for point-of-care approaches.
Collapse
Affiliation(s)
- Christina Sharkey
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, USA;
- Department of Surgery, Division of Urology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Rachel White
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, USA;
| | - Michael Finocchiaro
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, USA;
| | - Judene Thomas
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, USA;
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
| | - Jose Estevam
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, USA;
| | - Tania Konry
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, USA;
| |
Collapse
|
12
|
Zhang Y, Agresti JJ, Zheng Y, Weitz DA. High-throughput direct screening of restriction endonuclease using a microfluidic fluorescence-activated drop sorter based on the SOS response in Escherichia coli. Analyst 2024; 149:3575-3584. [PMID: 38758107 DOI: 10.1039/d4an00106k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
A restriction endonuclease (RE) is an enzyme that can recognize a specific DNA sequence and cleave that DNA into fragments with double-stranded breaks. This sequence-specific cleaving ability and its ease of use have made REs commonly used tools in molecular biology since their first isolation and characterization in 1970s. While artificial REs still face many challenges in large-scale synthesis and precise activity control for practical use, searching for new REs in natural samples remains a viable route to expanding the RE pool for fundamental research and industrial applications. In this paper, we propose a new strategy to search for REs in an efficient manner. We constructed a host bacterial cell to link the genotype of REs to the phenotype of β-galactosidase expression based on the bacterial SOS response, and used a high-throughput microfluidic platform to isolate, detect and sort the REs in microfluidic drops at a frequency of ∼800 drops per second. We employed this strategy to screen for the XbaI gene from the constructed libraries of varied sizes. In a single round of sorting, a 90-fold target enrichment was achieved within 1 h. Compared to conventional RE-screening methods, the direct screening approach that we propose excels at efficient search of desirable REs in natural samples - especially unculturable samples - and can be tailored to high-throughput screening of a wide range of genotoxic targets.
Collapse
Affiliation(s)
- Yizhe Zhang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA.
| | - Jeremy J Agresti
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA.
| | - Yu Zheng
- New England BioLabs, Inc., Ipswich, MA 01938, USA
| | - David A Weitz
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA.
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
| |
Collapse
|
13
|
Partipilo G, Bowman EK, Palmer EJ, Gao Y, Ridley RS, Alper HS, Keitz BK. Single-Cell Phenotyping of Extracellular Electron Transfer via Microdroplet Encapsulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598847. [PMID: 38915652 PMCID: PMC11195189 DOI: 10.1101/2024.06.13.598847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Electroactive organisms contribute to metal cycling, pollutant removal, and other redox-driven environmental processes. Studying this phenomenon in high-throughput is challenging since extracellular reduction cannot easily be traced back to its cell of origin within a mixed population. Here, we describe the development of a microdroplet emulsion system to enrich EET-capable organisms. We validated our system using the model electroactive organism S. oneidensis and describe the tooling of a benchtop microfluidic system for oxygen-limited processes. We demonstrated enrichment of EET-capable phenotypes from a mixed wild-type and EET-knockout population. As a proof-of-concept application, bacteria were collected from iron sedimentation from Town Lake (Austin, TX) and subjected to microdroplet enrichment. We observed an increase in EET-capable organisms in the sorted population that was distinct when compared to a population enriched in a bulk culture more closely akin to traditional techniques for discovering EET-capable bacteria. Finally, two bacterial species, C. sakazakii and V. fessus not previously shown to be electroactive, were further cultured and characterized for their ability to reduce channel conductance in an organic electrochemical transistor (OECT) and to reduce soluble Fe(III). We characterized two bacterial species not previously shown to exhibit electrogenic behavior. Our results demonstrate the utility of a microdroplet emulsions for identifying putative EET-capable bacteria and how this technology can be leveraged in tandem with existing methods.
Collapse
Affiliation(s)
- Gina Partipilo
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712
| | - Emily K. Bowman
- Interdisciplinary Life Sciences Graduate Program, University of Texas at Austin, Austin, TX, 78712
| | - Emma J. Palmer
- Civil, Architectural, and Environmental Engineering, University of Texas at Austin, Austin, TX, 78712
| | - Yang Gao
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712
| | - Rodney S. Ridley
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712
| | - Hal S. Alper
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712
| | - Benjamin K. Keitz
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712
| |
Collapse
|
14
|
Ribeiro ALJL, Pérez-Arnaiz P, Sánchez-Costa M, Pérez L, Almendros M, van Vliet L, Gielen F, Lim J, Charnock S, Hollfelder F, González-Pastor JE, Berenguer J, Hidalgo A. Thermostable in vitro transcription-translation compatible with microfluidic droplets. Microb Cell Fact 2024; 23:169. [PMID: 38858677 PMCID: PMC11165818 DOI: 10.1186/s12934-024-02440-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 05/25/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND In vitro expression involves the utilization of the cellular transcription and translation machinery in an acellular context to produce one or more proteins of interest and has found widespread application in synthetic biology and in pharmaceutical biomanufacturing. Most in vitro expression systems available are active at moderate temperatures, but to screen large libraries of natural or artificial genetic diversity for highly thermostable enzymes or enzyme variants, it is instrumental to enable protein synthesis at high temperatures. OBJECTIVES Develop an in vitro expression system operating at high temperatures compatible with enzymatic assays and with technologies that enable ultrahigh-throughput protein expression in reduced volumes, such as microfluidic water-in-oil (w/o) droplets. RESULTS We produced cell-free extracts from Thermus thermophilus for in vitro translation including thermostable enzymatic cascades for energy regeneration and a moderately thermostable RNA polymerase for transcription, which ultimately limited the temperature of protein synthesis. The yield was comparable or superior to other thermostable in vitro expression systems, while the preparation procedure is much simpler and can be suited to different Thermus thermophilus strains. Furthermore, these extracts have enabled in vitro expression in microfluidic droplets at high temperatures for the first time. CONCLUSIONS Cell-free extracts from Thermus thermophilus represent a simpler alternative to heavily optimized or pure component thermostable in vitro expression systems. Moreover, due to their compatibility with droplet microfluidics and enzyme assays at high temperatures, the reported system represents a convenient gateway for enzyme screening at higher temperatures with ultrahigh-throughput.
Collapse
Grants
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- BIO-2013-44963-R, RED2022-134755-T, CEX2021-001154-S Ministerio de Ciencia e Innovación
- BIO-2013-44963-R, RED2022-134755-T, CEX2021-001154-S Ministerio de Ciencia e Innovación
Collapse
Affiliation(s)
- Ana L J L Ribeiro
- Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC), Nicolás Cabrera 1, 28049, Madrid, Spain
- Instituto de Biología Molecular, Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049, Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Patricia Pérez-Arnaiz
- Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC), Nicolás Cabrera 1, 28049, Madrid, Spain
- Instituto de Biología Molecular, Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049, Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Mercedes Sánchez-Costa
- Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC), Nicolás Cabrera 1, 28049, Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Lara Pérez
- Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC), Nicolás Cabrera 1, 28049, Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Marcos Almendros
- Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC), Nicolás Cabrera 1, 28049, Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Liisa van Vliet
- Departament of Biochemistry, Cambridge University, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
- DropTech Ltd, 91 Canterbury Court, Cambridge, CB4 3QU, UK
| | - Fabrice Gielen
- DropTech Ltd, 91 Canterbury Court, Cambridge, CB4 3QU, UK
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Department of Physics and Astronomy, Faculty of Environment, Science and Economy, University of Exeter, Stocker Road, Exeter, EX4 4QL, UK
| | - Jesmine Lim
- Prozomix Ltd, Building 4, West End Ind. Estate, Haltwhistle, Northumberland, NE49 9HA, UK
| | - Simon Charnock
- Prozomix Ltd, Building 4, West End Ind. Estate, Haltwhistle, Northumberland, NE49 9HA, UK
| | - Florian Hollfelder
- Departament of Biochemistry, Cambridge University, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - J Eduardo González-Pastor
- Centro de Astrobiología (CAB), CSIC-INTA, Ctra de Torrejón a Ajalvir, Km 4, 28850, Torrejón de Ardoz, Spain
| | - José Berenguer
- Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC), Nicolás Cabrera 1, 28049, Madrid, Spain
- Instituto de Biología Molecular, Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049, Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Aurelio Hidalgo
- Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC), Nicolás Cabrera 1, 28049, Madrid, Spain.
- Instituto de Biología Molecular, Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049, Madrid, Spain.
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain.
| |
Collapse
|
15
|
Kasputis T, Hosmer KE, He Y, Chen J. Ensuring food safety: Microfluidic-based approaches for the detection of food contaminants. ANALYTICAL SCIENCE ADVANCES 2024; 5:e2400003. [PMID: 38948318 PMCID: PMC11210746 DOI: 10.1002/ansa.202400003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 07/02/2024]
Abstract
Detecting foodborne contamination is a critical challenge in ensuring food safety and preventing human suffering and economic losses. Contaminated food, comprising biological agents (e.g. bacteria, viruses and fungi) and chemicals (e.g. toxins, allergens, antibiotics and heavy metals), poses significant risks to public health. Microfluidic technology has emerged as a transformative solution, revolutionizing the detection of contaminants with precise and efficient methodologies. By manipulating minute volumes of fluid on miniaturized systems, microfluidics enables the creation of portable chips for biosensing applications. Advancements from early glass and silicon devices to modern polymers and cellulose-based chips have significantly enhanced microfluidic technology, offering adaptability, flexibility, cost-effectiveness and biocompatibility. Microfluidic systems integrate seamlessly with various biosensing reactions, facilitating nucleic acid amplification, target analyte recognition and accurate signal readouts. As research progresses, microfluidic technology is poised to play a pivotal role in addressing evolving challenges in the detection of foodborne contaminants. In this short review, we delve into various manufacturing materials for state-of-the-art microfluidic devices, including inorganics, elastomers, thermoplastics and paper. Additionally, we examine several applications where microfluidic technology offers unique advantages in the detection of food contaminants, including bacteria, viruses, fungi, allergens and more. This review underscores the significant advancement of microfluidic technology and its pivotal role in advancing the detection and mitigation of foodborne contaminants.
Collapse
Affiliation(s)
- Tom Kasputis
- Department of Biological Systems EngineeringVirginia TechBlacksburgVirginiaUSA
| | | | - Yawen He
- Department of Biological Systems EngineeringVirginia TechBlacksburgVirginiaUSA
| | - Juhong Chen
- Department of Biological Systems EngineeringVirginia TechBlacksburgVirginiaUSA
- Department of BioengineeringUniversity of CaliforniaRiversideCaliforniaUSA
| |
Collapse
|
16
|
Jain A, Stavrakis S, deMello A. Droplet-based microfluidics and enzyme evolution. Curr Opin Biotechnol 2024; 87:103097. [PMID: 38430713 DOI: 10.1016/j.copbio.2024.103097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Enzymes are widely used as catalysts in the chemical and pharmaceutical industries. While successful in many situations, they must usually be adapted to operate efficiently under nonnatural conditions. Enzyme engineering allows the creation of novel enzymes that are stable at elevated temperatures or have higher activities and selectivities. Current enzyme engineering techniques require the production and testing of enzyme variant libraries to identify members with desired attributes. Unfortunately, traditional screening methods cannot screen such large mutagenesis libraries in a robust and timely manner. Droplet-based microfluidic systems can produce, process, and sort picoliter droplets at kilohertz rates and have emerged as powerful tools for library screening and thus enzyme engineering. We describe how droplet-based microfluidics has been used to advance directed evolution.
Collapse
Affiliation(s)
- Ankit Jain
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland
| | - Andrew deMello
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland.
| |
Collapse
|
17
|
Yadav AS, Galogahi FM, Vashi A, Tran DT, Kijanka GS, Cha H, Sreejith KR, Nguyen NT. Synthesis and active manipulation of magnetic liquid beads. Biomed Microdevices 2024; 26:24. [PMID: 38709370 PMCID: PMC11074228 DOI: 10.1007/s10544-024-00708-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2024] [Indexed: 05/07/2024]
Abstract
We report the fabrication and characterisation of magnetic liquid beads with a solid magnetic shell and liquid core using microfluidic techniques. The liquid beads consist of a fluorinated oil core and a polymer shell with magnetite particles. The beads are generated in a flow-focusing polydimethylsiloxane (PDMS) device and cured by photo polymerisation. We investigated the response of the liquid beads to an external magnetic field by characterising their motion towards a permanent magnet. Magnetic sorting of liquid beads in a channel was achieved with 90% efficiency. The results show that the liquid beads can be controlled magnetically and have potential applications in digital microfluidics including nucleic acid amplification, drug delivery, cell culture, sensing, and tissue engineering. The present paper also discusses the magnetophoretic behaviour of the liquid bead by varying its mass and magnetite concentration in the shell. We also demonstrated the two-dimensional self-assembly of magnetic liquid beads for potential use in digital polymerase chain reaction and digital loop mediated isothermal amplification.
Collapse
Affiliation(s)
- Ajeet Singh Yadav
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Nathan, QLD, 4111, Australia
| | - Fariba Malekpour Galogahi
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Nathan, QLD, 4111, Australia
| | - Aditya Vashi
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Nathan, QLD, 4111, Australia
| | - Du Tuan Tran
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Nathan, QLD, 4111, Australia
| | - Gregor S Kijanka
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Nathan, QLD, 4111, Australia
| | - Haotian Cha
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Nathan, QLD, 4111, Australia
| | - Kamalalayam Rajan Sreejith
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Nathan, QLD, 4111, Australia
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Nathan, QLD, 4111, Australia.
| |
Collapse
|
18
|
Zhu L, Cui X, Jiang L, Fang F, Liu B. Application and prospect of microfluidic devices for rapid assay of cell activities in the tumor microenvironment. BIOMICROFLUIDICS 2024; 18:031506. [PMID: 38899164 PMCID: PMC11185871 DOI: 10.1063/5.0206058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024]
Abstract
The global impact of cancer on human health has raised significant concern. In this context, the tumor microenvironment (TME) plays a pivotal role in the tumorigenesis and malignant progression. In order to enhance the accuracy and efficacy of therapeutic outcomes, there is an imminent requirement for in vitro models that can accurately replicate the intricate characteristics and constituents of TME. Microfluidic devices exhibit notable advantages in investigating the progression and treatment of tumors and have the potential to become a novel methodology for evaluating immune cell activities in TME and assist clinicians in assessing the prognosis of patients. In addition, it shows great advantages compared to traditional cell experiments. Therefore, the review first outlines the applications and advantages of microfluidic chips in facilitating tumor cell culture, constructing TME and investigating immune cell activities. Second, the roles of microfluidic devices in the analysis of circulating tumor cells, tumor prognosis, and drug screening have also been mentioned. Moreover, a forward-looking perspective is discussed, anticipating the widespread clinical adoption of microfluidic devices in the future.
Collapse
Affiliation(s)
- Linjing Zhu
- Department of Genetics, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, China
| | - Xueling Cui
- Department of Genetics, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, China
| | - Lingling Jiang
- Department of Oral Comprehensive Therapy, Hospital of Stomatology, Jilin University, Changchun, Jilin 130021, China
| | - Fang Fang
- Department of Genetics, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, China
| | - Boyang Liu
- Author to whom correspondence should be addressed:
| |
Collapse
|
19
|
Lin S, Riaud A, Zhou J. Selective Sparse Sampling of Water Droplets in Oil with Acoustic Tweezers. ACS Sens 2024; 9:2066-2074. [PMID: 38627252 DOI: 10.1021/acssensors.4c00101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2024]
Abstract
In microfluidics, water droplets are often used as independent biochemical microreactor units, enabling the implementation of massively parallel screening assays where only a few of the reacting water droplets yield a positive result. However, sampling the product of these few successful reactions is an unsolved challenge. One possible solution is to use acoustic tweezers, which are lab-free, easily miniaturized, and biocompatible manipulation tools, and existing acoustic tweezers manipulating particles or cells, and water droplet manipulation in oil with an acoustic tweezer is absent. The first challenge in attempting to recover a few water droplets from a large batch is the selective manipulation of water droplets in an oil system. In this paper, we trap and manipulate single water droplets in oil using integrated single-beam (focused beam/vortex beam) acoustic tweezers for the first time. We find that water droplets with a diameter smaller than half a wavelength are trapped by acoustic vortices, while larger ones are better captured by focused acoustic beams. It is the first step to extract the target water droplet microreactors (positive ones) in an oil system and analyze their content. Compared to previous techniques, such as fluorescence-activated cell sorting (FACS), our technique is sparse, meaning that the sampling time is proportional to the number of droplets required and very insensitive to the total number of microreactors, making it well suited for large-scale screening assays.
Collapse
Affiliation(s)
- Siying Lin
- School of Microelectronics, Fudan University, Shanghai 200433, China
| | - Antoine Riaud
- School of Microelectronics, Fudan University, Shanghai 200433, China
| | - Jia Zhou
- School of Microelectronics, Fudan University, Shanghai 200433, China
| |
Collapse
|
20
|
Yan JD, Yang CY, Han A, Wu CC. A Label-Free Droplet Sorting Platform Integrating Dielectrophoretic Separation for Estimating Bacterial Antimicrobial Resistance. BIOSENSORS 2024; 14:218. [PMID: 38785691 PMCID: PMC11117925 DOI: 10.3390/bios14050218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
Antimicrobial resistance (AMR) has become a crucial global health issue. Antibiotic-resistant bacteria can survive after antibiotic treatments, lowering drug efficacy and increasing lethal risks. A microfluidic water-in-oil emulsion droplet system can entrap microorganisms and antibiotics within the tiny bioreactor, separate from the surroundings, enabling independent assays that can be performed in a high-throughput manner. This study presents the development of a label-free dielectrophoresis (DEP)-based microfluidic platform to sort droplets that co-encapsulate Escherichia coli (E. coli) and ampicillin (Amp) and droplets that co-encapsulate Amp-resistant (AmpR) E. coli with Amp only based on the conductivity-dependent DEP force (FDEP) without the assistance of optical analyses. The 9.4% low conductivity (LC) Luria-Bertani (LB) broth diluted with 170 mM mannitol can maintain E. coli and AmpR E. coli growth for 3 h and allow Amp to kill almost all E. coli, which can significantly increase the LCLB conductivity by about 100 μS/cm. Therefore, the AmpR E. coli/9.4%LCLB/Amp where no cells are killed and the E. coli/9.4%LCLB/Amp-containing droplets where most of the cells are killed can be sorted based on this conductivity difference at an applied electric field of 2 MHz and 100 Vpp that generates positive FDEP. Moreover, the sorting ratio significantly decreased to about 50% when the population of AmpR E. coli was equal to or higher than 50% in droplets. The conductivity-dependent DEP-based sorting platform exhibits promising potential to probe the ratio of AmpR E. coli in an unknown bacterial sample by using the sorting ratio as an index.
Collapse
Affiliation(s)
- Jia-De Yan
- Doctoral Program in Tissue Engineering and Regenerative Medicine, National Chung Hsing University, Taichung City 402, Taiwan;
| | - Chiou-Ying Yang
- Institute of Molecular Biology, National Chung Hsing University, Taichung City 402, Taiwan;
| | - Arum Han
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843, USA
- Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Ching-Chou Wu
- Doctoral Program in Tissue Engineering and Regenerative Medicine, National Chung Hsing University, Taichung City 402, Taiwan;
- Department of Bio-Industrial Mechatronics Engineering, National Chung Hsing University, Taichung City 402, Taiwan
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung City 402, Taiwan
| |
Collapse
|
21
|
Xin Y, Foster SW, Makey DM, Parker D, Bradow J, Wang X, Berritt S, Mongillo R, Grinias JP, Kennedy RT. High-Throughput Capillary Liquid Chromatography Using a Droplet Injection and Application to Reaction Screening. Anal Chem 2024; 96:4693-4701. [PMID: 38442211 PMCID: PMC11001260 DOI: 10.1021/acs.analchem.4c00150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
The cycle time of a standard liquid chromatography (LC) system is the sum of the time for the chromatographic run and the autosampler injection sequence. Although LC separation times in the 1-10 s range have been demonstrated, injection sequences are commonly >15 s, limiting throughput possible with LC separations. Further, such separations are performed on relatively large bore columns requiring flow rates of ≥5 mL/min, thus generating large volumes of mobile phase waste when used for large scale screening and increasing the difficulty in interfacing to mass spectrometry. Here, a droplet injector system was established that replaces the autosampler with a four-port, two-position valve equipped with a 20 nL internal loop interfaced to a syringe pump and a three-axis positioner to withdraw sample droplets from a well plate. In the system, sample and immiscible fluid are pulled alternately from a well plate into a capillary and then through the injection valve. The valve is actuated when sample fills the loop to allow sequential injection of samples at high throughput. Capillary LC columns with 300 μm inner diameter were used to reduce the consumption of mobile phase and sample. The system achieved 96 separations of 20 nL droplet samples containing 3 components in as little as 8.1 min with 5-s cycle time. This system was coupled to a mass spectrometer through an electrospray ionization source for high-throughput chemical reaction screening.
Collapse
Affiliation(s)
- Yue Xin
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Samuel W Foster
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Devin M Makey
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Deklin Parker
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - James Bradow
- Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06415, United States
| | - Xiaochun Wang
- Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06415, United States
| | - Simon Berritt
- Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06415, United States
| | - Robert Mongillo
- Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06415, United States
| | - James P Grinias
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Robert T Kennedy
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
22
|
Yan W, Li X, Zhao D, Xie M, Li T, Qian L, Ye C, Shi T, Wu L, Wang Y. Advanced strategies in high-throughput droplet screening for enzyme engineering. Biosens Bioelectron 2024; 248:115972. [PMID: 38171222 DOI: 10.1016/j.bios.2023.115972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/05/2023] [Accepted: 12/23/2023] [Indexed: 01/05/2024]
Abstract
Enzymes, as biocatalysts, play a cumulatively important role in environmental purification and industrial production of chemicals and pharmaceuticals. However, natural enzymes are limited by their physiological properties in practice, which need to be modified driven by requirements. Screening and isolating certain enzyme variants or ideal industrial strains with high yielding of target product enzymes is one of the main directions of enzyme engineering research. Droplet-based high-throughput screening (DHTS) technology employs massive monodisperse emulsion droplets as microreactors to achieve single strain encapsulation, as well as continuous monitoring for the inside mutant library. It can effectively sort out strains or enzymes with desired characteristics, offering a throughput of 108 events per hour. Much of the early literature focused on screening various engineered strains or designing signalling sorting strategies based on DHTS technology. However, the field of enzyme engineering lacks a comprehensive overview of advanced methods for microfluidic droplets and their cutting-edge developments in generation and manipulation. This review emphasizes the advanced strategies and frontiers of microfluidic droplet generation and manipulation facilitating enzyme engineering development. We also introduce design for various screening signals that cooperate with DHTS and devote to enzyme engineering.
Collapse
Affiliation(s)
- Wenxin Yan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Xiang Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Danshan Zhao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Meng Xie
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Ting Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Lu Qian
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China; Ministry of Education Key Laboratory of NSLSCS, Nanjing Normal University, Nanjing 210046, China.
| | - Tianqiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China.
| | - Lina Wu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China; Food Laboratory of Zhongyuan, Luohe, 462300, Henan, China.
| | - Yuetong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China.
| |
Collapse
|
23
|
Kandpal M, Varshney N, Rawal KS, Jha HC. Gut dysbiosis and neurological modalities: An engineering approach via proteomic analysis of gut-brain axis. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 140:199-248. [PMID: 38762270 DOI: 10.1016/bs.apcsb.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2024]
Abstract
The human gut microbiota is a complex and dynamic community of microorganisms, that influence metabolic, neurodevelopmental, and immune pathways. Microbial dysbiosis, characterized by changes in microbial diversity and relative abundances, is implicated in the development of various chronic neurological and neurodegenerative disorders. These disorders are marked by the accumulation of pathological protein aggregates, leading to the progressive loss of neurons and behavioural functions. Dysregulations in protein-protein interaction networks and signalling complexes, critical for normal brain function, are common in neurological disorders but challenging to unravel, particularly at the neuron and synapse-specific levels. To advance therapeutic strategies, a deeper understanding of neuropathogenesis, especially during the progressive disease phase, is needed. Biomarkers play a crucial role in identifying disease pathophysiology and monitoring disease progression. Proteomics, a powerful technology, shows promise in accelerating biomarker discovery and aiding in the development of novel treatments. In this chapter, we provide an in-depth overview of how proteomic techniques, utilizing various biofluid samples from patients with neurological conditions and diverse animal models, have contributed valuable insights into the pathogenesis of numerous neurological disorders. We also discuss the current state of research, potential challenges, and future directions in proteomic approaches to unravel neuro-pathological conditions.
Collapse
Affiliation(s)
- Meenakshi Kandpal
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Nidhi Varshney
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Kunal Sameer Rawal
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Hem Chandra Jha
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India; Centre for Rural Development & Technology, IIT Indore, Indore, India.
| |
Collapse
|
24
|
Porebski BT, Balmforth M, Browne G, Riley A, Jamali K, Fürst MJLJ, Velic M, Buchanan A, Minter R, Vaughan T, Holliger P. Rapid discovery of high-affinity antibodies via massively parallel sequencing, ribosome display and affinity screening. Nat Biomed Eng 2024; 8:214-232. [PMID: 37814006 DOI: 10.1038/s41551-023-01093-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 08/23/2023] [Indexed: 10/11/2023]
Abstract
Developing therapeutic antibodies is laborious and costly. Here we report a method for antibody discovery that leverages the Illumina HiSeq platform to, within 3 days, screen in the order of 108 antibody-antigen interactions. The method, which we named 'deep screening', involves the clustering and sequencing of antibody libraries, the conversion of the DNA clusters into complementary RNA clusters covalently linked to the instrument's flow-cell surface on the same location, the in situ translation of the clusters into antibodies tethered via ribosome display, and their screening via fluorescently labelled antigens. By using deep screening, we discovered low-nanomolar nanobodies to a model antigen using 4 × 106 unique variants from yeast-display-enriched libraries, and high-picomolar single-chain antibody fragment leads for human interleukin-7 directly from unselected synthetic repertoires. We also leveraged deep screening of a library of 2.4 × 105 sequences of the third complementarity-determining region of the heavy chain of an anti-human epidermal growth factor receptor 2 (HER2) antibody as input for a large language model that generated new single-chain antibody fragment sequences with higher affinity for HER2 than those in the original library.
Collapse
Affiliation(s)
| | | | | | - Aidan Riley
- Biologics Engineering, AstraZeneca, Cambridge, UK
| | | | - Maximillian J L J Fürst
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | | | | | - Ralph Minter
- Biologics Engineering, AstraZeneca, Cambridge, UK
- Alchemab Therapeutics, London, UK
| | | | | |
Collapse
|
25
|
Vanella R, Küng C, Schoepfer AA, Doffini V, Ren J, Nash MA. Understanding activity-stability tradeoffs in biocatalysts by enzyme proximity sequencing. Nat Commun 2024; 15:1807. [PMID: 38418512 PMCID: PMC10902396 DOI: 10.1038/s41467-024-45630-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 01/26/2024] [Indexed: 03/01/2024] Open
Abstract
Understanding the complex relationships between enzyme sequence, folding stability and catalytic activity is crucial for applications in industry and biomedicine. However, current enzyme assay technologies are limited by an inability to simultaneously resolve both stability and activity phenotypes and to couple these to gene sequences at large scale. Here we present the development of enzyme proximity sequencing, a deep mutational scanning method that leverages peroxidase-mediated radical labeling with single cell fidelity to dissect the effects of thousands of mutations on stability and catalytic activity of oxidoreductase enzymes in a single experiment. We use enzyme proximity sequencing to analyze how 6399 missense mutations influence folding stability and catalytic activity in a D-amino acid oxidase from Rhodotorula gracilis. The resulting datasets demonstrate activity-based constraints that limit folding stability during natural evolution, and identify hotspots distant from the active site as candidates for mutations that improve catalytic activity without sacrificing stability. Enzyme proximity sequencing can be extended to other enzyme classes and provides valuable insights into biophysical principles governing enzyme structure and function.
Collapse
Affiliation(s)
- Rosario Vanella
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland.
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.
| | - Christoph Küng
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Alexandre A Schoepfer
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
- National Center for Competence in Research (NCCR), Catalysis, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Vanni Doffini
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Jin Ren
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Michael A Nash
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland.
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.
- National Center for Competence in Research (NCCR), Molecular Systems Engineering, 4058, Basel, Switzerland.
- Swiss Nanoscience Institute, 4056, Basel, Switzerland.
| |
Collapse
|
26
|
Kurdadze T, Lamadie F, Nehme KA, Teychené S, Biscans B, Rodriguez-Ruiz I. On-Chip Photonic Detection Techniques for Non-Invasive In Situ Characterizations at the Microfluidic Scale. SENSORS (BASEL, SWITZERLAND) 2024; 24:1529. [PMID: 38475065 DOI: 10.3390/s24051529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
Microfluidics has emerged as a robust technology for diverse applications, ranging from bio-medical diagnostics to chemical analysis. Among the different characterization techniques that can be used to analyze samples at the microfluidic scale, the coupling of photonic detection techniques and on-chip configurations is particularly advantageous due to its non-invasive nature, which permits sensitive, real-time, high throughput, and rapid analyses, taking advantage of the microfluidic special environments and reduced sample volumes. Putting a special emphasis on integrated detection schemes, this review article explores the most relevant advances in the on-chip implementation of UV-vis, near-infrared, terahertz, and X-ray-based techniques for different characterizations, ranging from punctual spectroscopic or scattering-based measurements to different types of mapping/imaging. The principles of the techniques and their interest are discussed through their application to different systems.
Collapse
Affiliation(s)
- Tamar Kurdadze
- CEA, DES, ISEC, DMRC, Univ Montpellier, 30207 Bagnols-sur-Ceze, Marcoule, France
| | - Fabrice Lamadie
- CEA, DES, ISEC, DMRC, Univ Montpellier, 30207 Bagnols-sur-Ceze, Marcoule, France
| | - Karen A Nehme
- Laboratoire de Génie Chimique, CNRS, UMR 5503, 4 Allée Emile Monso, 31432 Toulouse, France
| | - Sébastien Teychené
- Laboratoire de Génie Chimique, CNRS, UMR 5503, 4 Allée Emile Monso, 31432 Toulouse, France
| | - Béatrice Biscans
- Laboratoire de Génie Chimique, CNRS, UMR 5503, 4 Allée Emile Monso, 31432 Toulouse, France
| | - Isaac Rodriguez-Ruiz
- Laboratoire de Génie Chimique, CNRS, UMR 5503, 4 Allée Emile Monso, 31432 Toulouse, France
| |
Collapse
|
27
|
Nan L, Zhang H, Weitz DA, Shum HC. Development and future of droplet microfluidics. LAB ON A CHIP 2024; 24:1135-1153. [PMID: 38165829 DOI: 10.1039/d3lc00729d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Over the past two decades, advances in droplet-based microfluidics have facilitated new approaches to process and analyze samples with unprecedented levels of precision and throughput. A wide variety of applications has been inspired across multiple disciplines ranging from materials science to biology. Understanding the dynamics of droplets enables optimization of microfluidic operations and design of new techniques tailored to emerging demands. In this review, we discuss the underlying physics behind high-throughput generation and manipulation of droplets. We also summarize the applications in droplet-derived materials and droplet-based lab-on-a-chip biotechnology. In addition, we offer perspectives on future directions to realize wider use of droplet microfluidics in industrial production and biomedical analyses.
Collapse
Affiliation(s)
- Lang Nan
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong, China
| | - Huidan Zhang
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - David A Weitz
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong, China
| | - Ho Cheung Shum
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong, China
| |
Collapse
|
28
|
López-Domene R, Manteca A, Rodriguez-Abetxuko A, Beloqui A, Cortajarena AL. In vitro Production of Hemin-Based Artificial Metalloenzymes. Chemistry 2024; 30:e202303254. [PMID: 38145337 DOI: 10.1002/chem.202303254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 12/26/2023]
Abstract
Developing enzyme alternatives is pivotal to improving and enabling new processes in biotechnology and industry. Artificial metalloenzymes (ArMs) are combinations of protein scaffolds with metal elements, such as metal nanoclusters or metal-containing molecules with specific catalytic properties, which can be customized. Here, we engineered an ArM based on the consensus tetratricopeptide repeat (CTPR) scaffold by introducing a unique histidine residue to coordinate the hemin cofactor. Our results show that this engineered system exhibits robust peroxidase-like catalytic activity driven by the hemin. The expression of the scaffold and subsequent coordination of hemin was achieved by recombinant expression in bulk and through in vitro transcription and translation systems in water-in-oil drops. The ability to synthesize this system in emulsio paves the way to improve its properties by means of droplet microfluidic screenings, facilitating the exploration of the protein combinatorial space to discover improved or novel catalytic activities.
Collapse
Affiliation(s)
- Rocío López-Domene
- Centre for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, E-20014, Spain
- POLYMAT and Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country UPV/EHU, Donostia-San Sebastián, E-20018, Spain
| | - Aitor Manteca
- Centre for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, E-20014, Spain
| | - Andoni Rodriguez-Abetxuko
- POLYMAT and Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country UPV/EHU, Donostia-San Sebastián, E-20018, Spain
| | - Ana Beloqui
- POLYMAT and Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country UPV/EHU, Donostia-San Sebastián, E-20018, Spain
- IKERBASQUE, Basque Foundation for Science, Plaza Euskadi 5, E-48009, Bilbao, Spain
| | - Aitziber L Cortajarena
- Centre for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, E-20014, Spain
- IKERBASQUE, Basque Foundation for Science, Plaza Euskadi 5, E-48009, Bilbao, Spain
| |
Collapse
|
29
|
Chen S, Yang Z, Zhong Z, Yu S, Zhou J, Li J, Du G, Zhang G. Ultrahigh-throughput screening-assisted in vivo directed evolution for enzyme engineering. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:9. [PMID: 38254175 PMCID: PMC10804518 DOI: 10.1186/s13068-024-02457-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024]
Abstract
BACKGROUND Classical directed evolution is a powerful approach for engineering biomolecules with improved or novel functions. However, it traditionally relies on labour- and time-intensive iterative cycles, due in part to the need for multiple molecular biology steps, including DNA transformation, and limited screening throughput. RESULTS In this study, we present an ultrahigh throughput in vivo continuous directed evolution system with thermosensitive inducible tunability, which is based on error-prone DNA polymerase expression modulated by engineered thermal-responsive repressor cI857, and genomic MutS mutant with temperature-sensitive defect for fixation of mutations in Escherichia coli. We demonstrated the success of the in vivo evolution platform with β-lactamase as a model, with an approximately 600-fold increase in the targeted mutation rate. Furthermore, the platform was combined with ultrahigh-throughput screening methods and employed to evolve α-amylase and the resveratrol biosynthetic pathway. After iterative rounds of enrichment, a mutant with a 48.3% improvement in α-amylase activity was identified via microfluidic droplet screening. In addition, when coupled with an in vivo biosensor in the resveratrol biosynthetic pathway, a variant with 1.7-fold higher resveratrol production was selected by fluorescence-activated cell sorting. CONCLUSIONS In this study, thermal-responsive targeted mutagenesis coupled with ultrahigh-throughput screening was developed for the rapid evolution of enzymes and biosynthetic pathways.
Collapse
Affiliation(s)
- Shuaili Chen
- Science Center for Future Foods, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Zhanhao Yang
- Science Center for Future Foods, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Ze Zhong
- Science Center for Future Foods, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Shiqin Yu
- Science Center for Future Foods, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Jingwen Zhou
- Science Center for Future Foods, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Engineering Research Center of Ministry of Education On Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Jianghua Li
- Science Center for Future Foods, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Engineering Research Center of Ministry of Education On Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Guocheng Du
- Science Center for Future Foods, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Engineering Research Center of Ministry of Education On Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
| | - Guoqiang Zhang
- Science Center for Future Foods, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Engineering Research Center of Ministry of Education On Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
| |
Collapse
|
30
|
Li X, Tang S, Zhang Y, Zhu J, Forgham H, Zhao C, Zhang C, Davis TP, Qiao R. Tailored Fluorosurfactants through Controlled/Living Radical Polymerization for Highly Stable Microfluidic Droplet Generation. Angew Chem Int Ed Engl 2024; 63:e202315552. [PMID: 38038248 PMCID: PMC10952479 DOI: 10.1002/anie.202315552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/01/2023] [Accepted: 12/01/2023] [Indexed: 12/02/2023]
Abstract
Droplet-based microfluidics represents a disruptive technology in the field of chemistry and biology through the generation and manipulation of sub-microlitre droplets. To avoid droplet coalescence, fluoropolymer-based surfactants are commonly used to reduce the interfacial tension between two immiscible phases to stabilize droplet interfaces. However, the conventional preparation of fluorosurfactants involves multiple steps of conjugation reactions between fluorinated and hydrophilic segments to form multiple-block copolymers. In addition, synthesis of customized surfactants with tailored properties is challenging due to the complex synthesis process. Here, we report a highly efficient synthetic method that utilizes living radical polymerization (LRP) to produce fluorosurfactants with tailored functionalities. Compared to the commercialized surfactant, our surfactants outperform in thermal cycling for polymerase chain reaction (PCR) testing, and exhibit exceptional biocompatibility for cell and yeast culturing in a double-emulsion system. This breakthrough synthetic approach has the potential to revolutionize the field of droplet-based microfluidics by enabling the development of novel designs that generate droplets with superior stability and functionality for a wide range of applications.
Collapse
Affiliation(s)
- Xiangke Li
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandBrisbane, Queensland4072Australia
| | - Shi‐Yang Tang
- School of Electronics and Computer ScienceUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Yang Zhang
- School of Engineering, Faculty of Science and EngineeringMacquarie UniversitySydney, NSW2109Australia
| | - Jiayuan Zhu
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandBrisbane, Queensland4072Australia
| | - Helen Forgham
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandBrisbane, Queensland4072Australia
| | - Chun‐Xia Zhao
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandBrisbane, Queensland4072Australia
- School of Chemical Engineering and Advanced MaterialsThe University of AdelaideAdelaide, SA5005Australia
| | - Cheng Zhang
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandBrisbane, Queensland4072Australia
| | - Thomas P. Davis
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandBrisbane, Queensland4072Australia
| | - Ruirui Qiao
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandBrisbane, Queensland4072Australia
| |
Collapse
|
31
|
Baranova MN, Pilipenko EA, Gabibov AG, Terekhov SS, Smirnov IV. Animal Microbiomes as a Source of Novel Antibiotic-Producing Strains. Int J Mol Sci 2023; 25:537. [PMID: 38203702 PMCID: PMC10779147 DOI: 10.3390/ijms25010537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/25/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Natural compounds continue to serve as the most fruitful source of new antimicrobials. Analysis of bacterial genomes have revealed that the biosynthetic potential of antibiotic producers by far exceeds the number of already discovered structures. However, due to the repeated discovery of known substances, it has become necessary to change both approaches to the search for antibiotics and the sources of producer strains. The pressure of natural selection and the diversity of interactions in symbiotic communities make animal microbiomes promising sources of novel substances. Here, microorganisms associated with various animals were examined in terms of their antimicrobial agents. The application of alternative cultivation techniques, ultrahigh-throughput screening, and genomic analysis facilitated the investigation of compounds produced by unique representatives of the animal microbiota. We believe that new strategies of antipathogen defense will be discovered by precisely studying cell-cell and host-microbe interactions in microbiomes in the wild.
Collapse
Affiliation(s)
- Margarita N. Baranova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
| | - Ekaterina A. Pilipenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
| | - Alexander G. Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Stanislav S. Terekhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ivan V. Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| |
Collapse
|
32
|
Zheng D, Zhang J, Jiang W, Xu Y, Meng H, Poh CL, Chen CH. Graphene oxide aptasensor droplet assay for detection of metabolites secreted by single cells applied to synthetic biology. LAB ON A CHIP 2023; 24:137-147. [PMID: 38054213 DOI: 10.1039/d3lc00959a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Synthetic biology harnesses the power of natural microbes by re-engineering metabolic pathways to manufacture desired compounds. Droplet technology has emerged as a high-throughput tool to screen single cells for synthetic biology, while the challenges in sensitive flexible single-cell secretion assay for bioproduction of high-value chemicals remained. Here, a novel droplet modifiable graphene oxide (GO) aptasensor was developed, enabling sensitive flexible detection of different target compounds secreted from single cells. Fluorophore-labeled aptamers were stably anchored on GO through π-π stacking interactions to minimize the non-specific interactions for low-background detection of target compounds with high signal-to-noise ratios. The assay's versatility was exhibited by adapting aptamer sequences to measure metabolic secretions like ATP and naringenin. To show the case, engineered E. coli were constructed for the bioproduction of naringenin. The high signal-to-noise ratio assay (∼2.72) was approached to precisely measure the naringenins secreted from single E. coli in the droplets. Consequently, secretory cells (Gib) were clearly distinguished from wild-type (WT) cells, with a low overlap in cell populations (∼0%) for bioproduction.
Collapse
Affiliation(s)
- Dan Zheng
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 117583, Singapore.
| | - Jingyun Zhang
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 117583, Singapore.
| | - Wenxin Jiang
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, China.
| | - Ying Xu
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, China.
| | - Haixu Meng
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, China.
| | - Chueh Loo Poh
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 117583, Singapore.
| | - Chia-Hung Chen
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, China.
- City University of Hong Kong Shenzhen Research Institute, Shenzhen Virtual University Park, Shenzhen, China
| |
Collapse
|
33
|
Pourmasoumi F, Hengoju S, Beck K, Stephan P, Klopfleisch L, Hoernke M, Rosenbaum MA, Kries H. Analysing Megasynthetase Mutants at High Throughput Using Droplet Microfluidics. Chembiochem 2023; 24:e202300680. [PMID: 37804133 DOI: 10.1002/cbic.202300680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/08/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) are giant enzymatic assembly lines that deliver many pharmaceutically valuable natural products, including antibiotics. As the search for new antibiotics motivates attempts to redesign nonribosomal metabolic pathways, more robust and rapid sorting and screening platforms are needed. Here, we establish a microfluidic platform that reliably detects production of the model nonribosomal peptide gramicidin S. The detection is based on calcein-filled sensor liposomes yielding increased fluorescence upon permeabilization. From a library of NRPS mutants, the sorting platform enriches the gramicidin S producer 14.5-fold, decreases internal stop codons 250-fold, and generates enrichment factors correlating with enzyme activity. Screening for NRPS activity with a reliable non-binary sensor will enable more sophisticated structure-activity studies and new engineering applications in the future.
Collapse
Affiliation(s)
- Farzaneh Pourmasoumi
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Sundar Hengoju
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Katharina Beck
- Faculty of Chemistry and Pharmacy, Albert-Ludwigs-Universität, Hermann-Herder-Str. 9, 79104, Freiburg i. Br., Germany
| | - Philipp Stephan
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Lukas Klopfleisch
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Maria Hoernke
- Faculty of Chemistry and Pharmacy, Albert-Ludwigs-Universität, Hermann-Herder-Str. 9, 79104, Freiburg i. Br., Germany
- Faculty of Chemistry, Martin-Luther-Universität, Von-Danckelmann-Platz 4, 06108, Halle (S.), Germany
| | - Miriam A Rosenbaum
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
- Department of Chemistry, University of Bayreuth, Universitätsstrasse 30, 95440, Bayreuth, Germany
| |
Collapse
|
34
|
Ornelas MY, Cournoyer JE, Bram S, Mehta AP. Evolution and synthetic biology. Curr Opin Microbiol 2023; 76:102394. [PMID: 37801925 PMCID: PMC10842511 DOI: 10.1016/j.mib.2023.102394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 08/29/2023] [Accepted: 09/08/2023] [Indexed: 10/08/2023]
Abstract
Evolutionary observations have often served as an inspiration for biological design. Decoding of the central dogma of life at a molecular level and understanding of the cellular biochemistry have been elegantly used to engineer various synthetic biology applications, including building genetic circuits in vitro and in cells, building synthetic translational systems, and metabolic engineering in cells to biosynthesize and even bioproduce complex high-value molecules. Here, we review three broad areas of synthetic biology that are inspired by evolutionary observations: (i) combinatorial approaches toward cell-based biomolecular evolution, (ii) engineering interdependencies to establish microbial consortia, and (iii) synthetic immunology. In each of the areas, we will highlight the evolutionary premise that was central toward designing these platforms. These are only a subset of the examples where evolution and natural phenomena directly or indirectly serve as a powerful source of inspiration in shaping synthetic biology and biotechnology.
Collapse
Affiliation(s)
- Marya Y Ornelas
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Matthews Avenue, Urbana, IL 61801, United States
| | - Jason E Cournoyer
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Matthews Avenue, Urbana, IL 61801, United States
| | - Stanley Bram
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Matthews Avenue, Urbana, IL 61801, United States
| | - Angad P Mehta
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Matthews Avenue, Urbana, IL 61801, United States; Institute for Genomic Biology, University of Illinois at Urbana, Champaign, United States; Cancer Center at Illinois, University of Illinois at Urbana, Champaign, United States.
| |
Collapse
|
35
|
Makey DM, Diehl RC, Xin Y, Murray BE, Stoll DR, Ruotolo BT, Grinias JP, Narayan ARH, Lopez-Carillo V, Stark M, Johnen P, Kennedy RT. High-Throughput Liquid Chromatographic Analysis Using a Segmented Flow Injector with a 1 s Cycle Time. Anal Chem 2023; 95:17028-17036. [PMID: 37943345 PMCID: PMC11027085 DOI: 10.1021/acs.analchem.3c03719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
High-throughput screening (HTS) workflows are revolutionizing many fields, including drug discovery, reaction discovery and optimization, diagnostics, sensing, and enzyme engineering. Liquid chromatography (LC) is commonly deployed during HTS to reduce matrix effects, distinguish isomers, and preconcentrate prior to detection, but LC separation time often limits throughput. Although subsecond LC separations have been demonstrated, they are rarely utilized during HTS due to limitations associated with the speed of common autosamplers. In this work, these limits are overcome by utilizing droplet microfluidics for sample introduction. In the method, a train of samples segmented by air are continuously pumped into the inlet of an LC injection valve that is actuated once each sample fills the sample loop. Coupled with 2.1 mm diameter × 5 mm long columns packed with 2.7 μm superficially porous C18 particles operated at 5 mL/min, the injector enabled separation of 3 components at 1 s/sample and analysis of a 96-well plate in 1.6 min with <2% peak area relative standard deviation. Analyte-dependent carryover was minimized by including wash droplets composed of organic solvent in between sample droplets. High-throughput LC coupled with mass spectrometric detection using the segmented flow injector was applied to a screen of inhibitors of a cytochrome P450-catalyzed hydroxylation reaction. Measurements of the reaction substrate and product concentrations made using fast LC with the segmented flow injector correlated well with measurements made using a more conventional, 3 min LC method. These results demonstrate the potential for droplet microfluidics to be used for sample introduction during high-throughput LC analysis.
Collapse
Affiliation(s)
- Devin M Makey
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Roger C Diehl
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yue Xin
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bridget E Murray
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Dwight R Stoll
- Department of Chemistry, Gustavus Adolphus College, Saint Peter, Minnesota 56082, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - James P Grinias
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Alison R H Narayan
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | - Robert T Kennedy
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
36
|
Elias M, Guan X, Hudson D, Bose R, Kwak J, Petrounia I, Touah K, Mansour S, Yue P, Errasti G, Delacroix T, Ghosh A, Chakrabarti R. Evolution of Organic Solvent-Resistant DNA Polymerases. ACS Synth Biol 2023; 12:3170-3188. [PMID: 37611245 DOI: 10.1021/acssynbio.2c00515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
The introduction of thermostable polymerases revolutionized the polymerase chain reaction (PCR) and biotechnology. However, many GC-rich genes cannot be PCR-amplified with high efficiency in water, irrespective of temperature. Although polar organic cosolvents can enhance nucleic acid polymerization and amplification by destabilizing duplex DNA and secondary structures, nature has not selected for the evolution of solvent-tolerant polymerase enzymes. Here, we used ultrahigh-throughput droplet-based selection and deep sequencing along with computational free-energy and binding affinity calculations to evolve Taq polymerase to generate enzymes that are both stable and highly active in the presence of organic cosolvents, resulting in up to 10% solvent resistance and over 100-fold increase in stability at 97.5 °C in the presence of 1,4-butanediol, as well as tolerance to up to 10 times higher concentrations of the potent cosolvents sulfolane and 2-pyrrolidone. Using these polymerases, we successfully amplified a broad spectrum of GC-rich templates containing regions with over 90% GC content, including templates recalcitrant to amplification with existing polymerases, even in the presence of cosolvents. We also demonstrated dramatically reduced GC bias in the amplification of genes with widely varying GC content in quantitative polymerase chain reaction (qPCR). By expanding the scope of solvent systems compatible with nucleic acid polymerization, these organic solvent-resistant polymerases enable a dramatic reduction of sequence bias not achievable through thermal resistance alone, with significant implications for a wide range of applications including sequencing and synthetic biology in mixed aqueous-organic media.
Collapse
Affiliation(s)
- Mohammed Elias
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
| | - Xiangying Guan
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
| | - Devin Hudson
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
| | - Rahul Bose
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
| | - Joon Kwak
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
| | - Ioanna Petrounia
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
| | - Kenza Touah
- Center for Protein Engineering & Drug Discovery, PMC Isochem SAS, 32 Rue Lavoisier, Vert-Le-Petit 91710, France
| | - Sourour Mansour
- Center for Protein Engineering & Drug Discovery, PMC Isochem SAS, 32 Rue Lavoisier, Vert-Le-Petit 91710, France
| | - Peng Yue
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
| | - Gauthier Errasti
- Center for Protein Engineering & Drug Discovery, PMC Isochem SAS, 32 Rue Lavoisier, Vert-Le-Petit 91710, France
| | - Thomas Delacroix
- Center for Protein Engineering & Drug Discovery, PMC Isochem SAS, 32 Rue Lavoisier, Vert-Le-Petit 91710, France
| | - Anisha Ghosh
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
- McGill University, 845 Rue Sherbrooke Ouest, Montreal, QC H3A 0G4, Canada
| | - Raj Chakrabarti
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
- Center for Protein Engineering & Drug Discovery, PMC Isochem SAS, 32 Rue Lavoisier, Vert-Le-Petit 91710, France
| |
Collapse
|
37
|
Diao Z, Wang X, Zhang J, Ge A, Xu T, Kan L, Li Y, Ji Y, Jing X, Xu J, Ma B. Optical-based microbubble for on-demand droplet release from static droplet array (SDA) for dispensing one droplet into one tube. Biosens Bioelectron 2023; 240:115639. [PMID: 37660461 DOI: 10.1016/j.bios.2023.115639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/05/2023]
Abstract
Static droplet array (SDA) is a pivotal tool for high-capacity screening assays, yet extraction and collection the target droplets that contain unique analytes or cells from the SDA remains one major technical bottleneck that limits its broader application. Here we present an optical-based on-demand droplet release (OODR) system by incorporating a 1064 nm laser-responsive indium tin oxide (ITO) layer into a chamber array-based droplet microfluidic chip. By focusing the 1064 nm laser onto the ITO layer, microbubbles can be created via local heating to selectively push-out the droplets from the chamber. Then the released droplet is readily exported in a one-droplet-one-tube (ODOT) manner by the inherent capillary force into pipette tip. Releasing of the droplets containing fluorescein sodium demonstrated ∼100% successful rate (9 out of 6400 droplets were successfully released) and low residual (only ∼5% of the droplet volume remains in the chamber). White or fluorescence image-based releasing of single-cell-droplets directly after cell loading or multi-cells-droplets derived from on-chip single-cell cultivation for both E. coli and yeast cells further demonstrated the wide applicability of OODR. The present system is user-friendly and has the potential to be applied in various high-throughput screening assays, including single molecule/cell analysis, drug screening, and phenotype-based cell sorting.
Collapse
Affiliation(s)
- Zhidian Diao
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Xixian Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Jiaping Zhang
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Anle Ge
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Teng Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Lingyan Kan
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Yuandong Li
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Yuetong Ji
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Qingdao Single-Cell Biotech., Co., Ltd., Qingdao, China
| | - Xiaoyan Jing
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China.
| | - Bo Ma
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China.
| |
Collapse
|
38
|
Luu XC, Shida Y, Suzuki Y, Kuwahara D, Fujimoto T, Takahashi Y, Sato N, Nakamura A, Ogasawara W. Ultrahigh-throughput screening of Trichoderma reesei strains capable of carbon catabolite repression release and cellulase hyperproduction using a microfluidic droplet platform. Biosci Biotechnol Biochem 2023; 87:1393-1406. [PMID: 37550222 DOI: 10.1093/bbb/zbad108] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/28/2023] [Indexed: 08/09/2023]
Abstract
Trichoderma reesei is the most well-known cellulase producer in the biorefinery industry. Its cellulase biosynthesis is repressed by glucose via carbon catabolite repression (CCR), making CCR-releasing strains with cellulase hyperproduction desirable. Here, we employed a microfluidic droplet platform to culture and screen T. reesei mutants capable of CCR release and cellulase overproduction from extensive mutagenesis libraries. With 3 mutagenesis rounds, about 6.20 × 103 droplets were sorted from a population of 1.51 × 106 droplets in a period of 4.4 h; 76 recovery mutants were screened on flask fermentation, and 2 glucose uptake retarded mutants, MG-9-3 and MG-9-3-30, were eventually isolated. We also generated a hypercellulase producer, M-5, with CCR release via a single mutagenesis round. The hyphal morphology and molecular mechanisms in the mutants were analyzed. This versatile approach combined with a comprehensive understanding of CCR release mechanisms will provide innovative and effective strategies for low-cost cellulase production.
Collapse
Affiliation(s)
- Xuan Chinh Luu
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, Japan
| | - Yosuke Shida
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, Japan
| | - Yoshiyuki Suzuki
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, Japan
| | - Daiki Kuwahara
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, Japan
| | - Takeshi Fujimoto
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, Japan
| | - Yuka Takahashi
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, Japan
| | - Naomi Sato
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, Japan
| | - Akihiro Nakamura
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, Japan
| | - Wataru Ogasawara
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, Japan
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, Japan
| |
Collapse
|
39
|
Mayer T, Givelet L, Simmel FC. Micro-compartmentalized strand displacement reactions with a random pool background. Interface Focus 2023; 13:20230011. [PMID: 37577002 PMCID: PMC10415739 DOI: 10.1098/rsfs.2023.0011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 06/26/2023] [Indexed: 08/15/2023] Open
Abstract
Toehold-mediated strand displacement (TMSD) is a widely used process in dynamic DNA nanotechnology, which has been applied for the actuation of molecular devices, in biosensor applications, and for DNA-based molecular computation. Similar processes also occur in a biological context, when RNA strands invade secondary structures or duplexes of other RNA or DNA molecules. Complex reaction environments-inside cells or synthetic cells-potentially contain a large number of competing nucleic acid molecules that transiently bind to the components of the strand displacement reaction of interest and thus slow down its kinetics. Here, we investigate the kinetics of TMSD reactions compartmentalized into water-in-oil emulsion droplets-in both the presence and absence of a random sequence background-using a droplet microfluidic 'stopped flow' set-up. The set-up enables one to determine the kinetics within thousands of droplets and easily vary experimental parameters such as the stoichiometry of the TMSD components. While the average kinetics in the droplets coincides precisely with the bulk behaviour, we observe considerable variability among the droplets. This variability is partially explained by the encapsulation procedure itself, but appears to be more pronounced in reactions involving a random pool background.
Collapse
Affiliation(s)
- Thomas Mayer
- Department of Bioscience, School of Natural Sciences, Technical University Munich, Garching, Germany
| | - Louis Givelet
- Department of Bioscience, School of Natural Sciences, Technical University Munich, Garching, Germany
| | - Friedrich C. Simmel
- Department of Bioscience, School of Natural Sciences, Technical University Munich, Garching, Germany
| |
Collapse
|
40
|
Raza MH, Desai S, Aravamudhan S, Zadegan R. An outlook on the current challenges and opportunities in DNA data storage. Biotechnol Adv 2023; 66:108155. [PMID: 37068530 PMCID: PMC11060094 DOI: 10.1016/j.biotechadv.2023.108155] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/23/2023] [Accepted: 04/12/2023] [Indexed: 04/19/2023]
Abstract
Silicon is the gold standard for information storage systems. The exponential generation of digital information will exhaust the global supply of refined silicon. Therefore, investing in alternative information storage materials such as DNA has gained momentum. DNA as a memory material possesses several advantages over silicon-based data storage, including higher storage capacity, data retention, and lower operational energy. Routine DNA data storage approaches encode data into chemically synthesized nucleotide sequences. The scalability of DNA data storage depends on factors such as the cost and the generation of hazardous waste during DNA synthesis, latency of writing and reading, and limited rewriting capacity. Here, we review the current status of DNA data storage encoding, writing, storing, retrieving and reading, and discuss the technology's challenges and opportunities.
Collapse
Affiliation(s)
- Muhammad Hassan Raza
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, Greensboro, NC 27401, USA
| | - Salil Desai
- Department of Industrial & Systems Engineering, North Carolina Agricultural & Technical State University, Greensboro, NC 27411, USA; Center of Excellence in Product Design and Advanced Manufacturing (CEPDAM), North Carolina Agricultural & Technical State University, Greensboro, NC 27411, USA
| | - Shyam Aravamudhan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, Greensboro, NC 27401, USA; Center of Excellence in Product Design and Advanced Manufacturing (CEPDAM), North Carolina Agricultural & Technical State University, Greensboro, NC 27411, USA
| | - Reza Zadegan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, Greensboro, NC 27401, USA; Center of Excellence in Product Design and Advanced Manufacturing (CEPDAM), North Carolina Agricultural & Technical State University, Greensboro, NC 27411, USA.
| |
Collapse
|
41
|
Zhang XE, Liu C, Dai J, Yuan Y, Gao C, Feng Y, Wu B, Wei P, You C, Wang X, Si T. Enabling technology and core theory of synthetic biology. SCIENCE CHINA. LIFE SCIENCES 2023; 66:1742-1785. [PMID: 36753021 PMCID: PMC9907219 DOI: 10.1007/s11427-022-2214-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/04/2022] [Indexed: 02/09/2023]
Abstract
Synthetic biology provides a new paradigm for life science research ("build to learn") and opens the future journey of biotechnology ("build to use"). Here, we discuss advances of various principles and technologies in the mainstream of the enabling technology of synthetic biology, including synthesis and assembly of a genome, DNA storage, gene editing, molecular evolution and de novo design of function proteins, cell and gene circuit engineering, cell-free synthetic biology, artificial intelligence (AI)-aided synthetic biology, as well as biofoundries. We also introduce the concept of quantitative synthetic biology, which is guiding synthetic biology towards increased accuracy and predictability or the real rational design. We conclude that synthetic biology will establish its disciplinary system with the iterative development of enabling technologies and the maturity of the core theory.
Collapse
Affiliation(s)
- Xian-En Zhang
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Chenli Liu
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Junbiao Dai
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Yingjin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Bian Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ping Wei
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Xiaowo Wang
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Tong Si
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| |
Collapse
|
42
|
Cardoso BD, Castanheira EMS, Lanceros-Méndez S, Cardoso VF. Recent Advances on Cell Culture Platforms for In Vitro Drug Screening and Cell Therapies: From Conventional to Microfluidic Strategies. Adv Healthc Mater 2023; 12:e2202936. [PMID: 36898671 DOI: 10.1002/adhm.202202936] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/27/2023] [Indexed: 03/12/2023]
Abstract
The clinical translations of drugs and nanomedicines depend on coherent pharmaceutical research based on biologically accurate screening approaches. Since establishing the 2D in vitro cell culture method, the scientific community has improved cell-based drug screening assays and models. Those advances result in more informative biochemical assays and the development of 3D multicellular models to describe the biological complexity better and enhance the simulation of the in vivo microenvironment. Despite the overall dominance of conventional 2D and 3D cell macroscopic culture methods, they present physicochemical and operational challenges that impair the scale-up of drug screening by not allowing a high parallelization, multidrug combination, and high-throughput screening. Their combination and complementarity with microfluidic platforms enable the development of microfluidics-based cell culture platforms with unequivocal advantages in drug screening and cell therapies. Thus, this review presents an updated and consolidated view of cell culture miniaturization's physical, chemical, and operational considerations in the pharmaceutical research scenario. It clarifies advances in the field using gradient-based microfluidics, droplet-based microfluidics, printed-based microfluidics, digital-based microfluidics, SlipChip, and paper-based microfluidics. Finally, it presents a comparative analysis of the performance of cell-based methods in life research and development to achieve increased precision in the drug screening process.
Collapse
Affiliation(s)
- Beatriz D Cardoso
- Physics Centre of Minho and Porto Universities (CF-UM-UP), Campus de Gualtar, University of Minho, Braga, 4710-057, Portugal
- LaPMET-Laboratory of Physics for Materials and Emergent Technologies, University of Minho, 4710-057, Braga, Portugal
- Center for MicroElectromechanical Systems (CMEMS-UMinho), Campus de Azurém, University of Minho, 4800-058, Guimarães, Portugal
- LABBELS-Associate Laboratory in Biotechnology and Bioengineering and Microelectromechanical Systems, University of Minho, Braga/Guimarães, Portugal
| | - Elisabete M S Castanheira
- Physics Centre of Minho and Porto Universities (CF-UM-UP), Campus de Gualtar, University of Minho, Braga, 4710-057, Portugal
- LaPMET-Laboratory of Physics for Materials and Emergent Technologies, University of Minho, 4710-057, Braga, Portugal
| | - Senentxu Lanceros-Méndez
- Physics Centre of Minho and Porto Universities (CF-UM-UP), Campus de Gualtar, University of Minho, Braga, 4710-057, Portugal
- LaPMET-Laboratory of Physics for Materials and Emergent Technologies, University of Minho, 4710-057, Braga, Portugal
- BCMaterials, Basque Center for Materials, Applications and Nanostructures, UPV/EHU Science Park, Leioa, 48940, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, 48009, Spain
| | - Vanessa F Cardoso
- Center for MicroElectromechanical Systems (CMEMS-UMinho), Campus de Azurém, University of Minho, 4800-058, Guimarães, Portugal
- LABBELS-Associate Laboratory in Biotechnology and Bioengineering and Microelectromechanical Systems, University of Minho, Braga/Guimarães, Portugal
| |
Collapse
|
43
|
Guan Y, Zhang H, Yan Z, Wei X, Zhang Z, Chen X. Surface Modification of Cyclic-Olefin-Copolymer (COC)-Based Microchannels for the Large-Scale Industrial Production of Droplet Microfluidic Devices. Bioengineering (Basel) 2023; 10:763. [PMID: 37508790 PMCID: PMC10376149 DOI: 10.3390/bioengineering10070763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/09/2023] [Accepted: 06/15/2023] [Indexed: 07/30/2023] Open
Abstract
The copolymers of cycloolefin (COC), a type of thermoplastic material, have been widely used for the large-scale industrial fabrication of droplet microfluidic devices, which is often performed using hot-embossing or injection-molding techniques. The generation of droplets and the uniformity of droplet sizes are significantly affected by the surface wettability of COC during fabrication and the pressure stability of the employed fluid pump during operation. In order to alleviate the effects of undesirable surface wettability and pressure variation on the generation of droplets in COC-based devices, a simple surface modification procedure was applied to hydrophobically modify the surfaces of COC-based microchannels for large-scale industrial production. The surface modification procedure consisted of an oxygen plasma treatment of the polymer surface followed by a solution-phase reaction in fluorocarbon solvent. The experimental results demonstrate that following the proposed surface modification, the COC droplet microfluidic devices could stably generate microvolume water droplets with a small coefficient of variation, even if the pressure of the dispersed phase (water) fluctuated. The durability test results regarding the modified surfaces show that the hydrophobicity of the modified COC surfaces could be sustained for up to four months, deteriorating with time thereafter. Our study can provide a potential solution useful in and guidance for the large-scale industrial production of droplet microfluidic devices for various applications, including polymerase chain reaction and single-cell analysis.
Collapse
Affiliation(s)
- Yefeng Guan
- Key Laboratory of Biomaterials of Guangdong Higher Education Institutes, Department of Biomedical Engineering, Jinan University, Guangzhou 510632, China
- Guangdong Shunde Innovative Design Institute, Foshan 528300, China
| | - Huiru Zhang
- Guangdong Shunde Innovative Design Institute, Foshan 528300, China
- Guangdong Foshan Lianchuang Graduate of Engineering, Foshan 528300, China
| | - Zhibin Yan
- Guangdong Provincial Key Laboratory of Optical Information Materials and Technology & Institute of Electronic Paper Displays, South China Academy of Advanced Optoelectronics, South China Normal University, Guangzhou 510006, China
| | - Xue Wei
- Key Laboratory of Biomaterials of Guangdong Higher Education Institutes, Department of Biomedical Engineering, Jinan University, Guangzhou 510632, China
| | - Zhuo Zhang
- Guangdong Shunde Innovative Design Institute, Foshan 528300, China
| | - Xuelian Chen
- Guangdong Shunde Innovative Design Institute, Foshan 528300, China
- Guangdong Provincial Key Laboratory of Optical Information Materials and Technology & Institute of Electronic Paper Displays, South China Academy of Advanced Optoelectronics, South China Normal University, Guangzhou 510006, China
| |
Collapse
|
44
|
Lai YK, Kao YT, Hess JF, Calabrese S, von Stetten F, Paust N. Interfacing centrifugal microfluidics with linear-oriented 8-tube strips and multichannel pipettes for increased throughput of digital assays. LAB ON A CHIP 2023; 23:2623-2632. [PMID: 37158238 DOI: 10.1039/d3lc00339f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
We present a centrifugal microfluidic cartridge for the eight-fold parallel generation of monodisperse water-in-oil droplets using standard laboratory equipment. The key element is interfacing centrifugal microfluidics with its design based on polar coordinates to the linear structures of standard high-throughput laboratory automation. Centrifugal step emulsification is used to simultaneously generate droplets from eight samples directly into standard 200 μl PCR 8-tube strips. To ensure minimal manual liquid handling, the design of the inlets allows the user to load the samples and the oil via a standard multichannel pipette. Simulation-based design of the cartridge ensures that the performance is consistent in each droplet generation unit despite the varying radial positions that originate from the interface to the linear oriented PCR 8-tube strip and from the integration of linear oriented inlet holes for the multichannel pipettes. Within 10 minutes, sample volumes of 50 μl per droplet generation unit are emulsified at a fixed rotation speed of 960 rpm into 1.47 × 105 monodisperse droplets with a mean diameter of 86 μm. The overall coefficient of variation (CV) of the droplet diameter was below 4%. Feasibility is demonstrated by an exemplary digital droplet polymerase chain reaction (ddPCR) assay which showed high linearity (R2 ≥ 0.999) across all of the eight tubes of the strip.
Collapse
Affiliation(s)
- Yu-Kai Lai
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Yu-Ting Kao
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Jacob Friedrich Hess
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Silvia Calabrese
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.
| | - Felix von Stetten
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Nils Paust
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| |
Collapse
|
45
|
Zhang L, Parvin R, Chen M, Hu D, Fan Q, Ye F. High-throughput microfluidic droplets in biomolecular analytical system: A review. Biosens Bioelectron 2023; 228:115213. [PMID: 36906989 DOI: 10.1016/j.bios.2023.115213] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/13/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023]
Abstract
Droplet microfluidic technology has revolutionized biomolecular analytical research, as it has the capability to reserve the genotype-to-phenotype linkage and assist for revealing the heterogeneity. Massive and uniform picolitre droplets feature dividing solution to the level that single cell and single molecule in each droplet can be visualized, barcoded, and analyzed. Then, the droplet assays can unfold intensive genomic data, offer high sensitivity, and screen and sort from a large number of combinations or phenotypes. Based on these unique advantages, this review focuses on up-to-date research concerning diverse screening applications utilizing droplet microfluidic technology. The emerging progress of droplet microfluidic technology is first introduced, including efficient and scaling-up in droplets encapsulation, and prevalent batch operations. Then the new implementations of droplet-based digital detection assays and single-cell muti-omics sequencing are briefly examined, along with related applications such as drug susceptibility testing, multiplexing for cancer subtype identification, interactions of virus-to-host, and multimodal and spatiotemporal analysis. Meanwhile, we specialize in droplet-based large-scale combinational screening regarding desired phenotypes, with an emphasis on sorting for immune cells, antibodies, enzymatic properties, and proteins produced by directed evolution methods. Finally, some challenges, deployment and future perspective of droplet microfluidics technology in practice are also discussed.
Collapse
Affiliation(s)
- Lexiang Zhang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Rokshana Parvin
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Mingshuo Chen
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Dingmeng Hu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Qihui Fan
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China; Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Fangfu Ye
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China; Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
| |
Collapse
|
46
|
Jiang J, Yang G, Ma F. Fluorescence coupling strategies in fluorescence-activated droplet sorting (FADS) for ultrahigh-throughput screening of enzymes, metabolites, and antibodies. Biotechnol Adv 2023; 66:108173. [PMID: 37169102 DOI: 10.1016/j.biotechadv.2023.108173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/17/2023] [Accepted: 05/06/2023] [Indexed: 05/13/2023]
Abstract
Fluorescence-activated droplet sorting (FADS) has emerged as a powerful tool for ultrahigh-throughput screening of enzymes, metabolites, and antibodies. Fluorescence coupling strategies (FCSs) are key to the development of new FADS methods through their coupling of analyte properties such as concentration, activities, and affinity with fluorescence signals. Over the last decade, a series of FCSs have been developed, greatly expanding applications of FADS. Here, we review recent advances in FCS for different analyte types, providing a critical comparison of the available FCSs and further classification into four categories according to their principles. We also summarize successful FADS applications employing FCSs in enzymes, metabolites, and antibodies. Further, we outline possible future developments in this area.
Collapse
Affiliation(s)
- Jingjie Jiang
- Medical Enzyme Engineering Center, CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
| | - Guangyu Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Fuqiang Ma
- Medical Enzyme Engineering Center, CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China.
| |
Collapse
|
47
|
Gantz M, Neun S, Medcalf EJ, van Vliet LD, Hollfelder F. Ultrahigh-Throughput Enzyme Engineering and Discovery in In Vitro Compartments. Chem Rev 2023; 123:5571-5611. [PMID: 37126602 PMCID: PMC10176489 DOI: 10.1021/acs.chemrev.2c00910] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Novel and improved biocatalysts are increasingly sourced from libraries via experimental screening. The success of such campaigns is crucially dependent on the number of candidates tested. Water-in-oil emulsion droplets can replace the classical test tube, to provide in vitro compartments as an alternative screening format, containing genotype and phenotype and enabling a readout of function. The scale-down to micrometer droplet diameters and picoliter volumes brings about a >107-fold volume reduction compared to 96-well-plate screening. Droplets made in automated microfluidic devices can be integrated into modular workflows to set up multistep screening protocols involving various detection modes to sort >107 variants a day with kHz frequencies. The repertoire of assays available for droplet screening covers all seven enzyme commission (EC) number classes, setting the stage for widespread use of droplet microfluidics in everyday biochemical experiments. We review the practicalities of adapting droplet screening for enzyme discovery and for detailed kinetic characterization. These new ways of working will not just accelerate discovery experiments currently limited by screening capacity but profoundly change the paradigms we can probe. By interfacing the results of ultrahigh-throughput droplet screening with next-generation sequencing and deep learning, strategies for directed evolution can be implemented, examined, and evaluated.
Collapse
Affiliation(s)
- Maximilian Gantz
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Stefanie Neun
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Elliot J Medcalf
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Liisa D van Vliet
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| |
Collapse
|
48
|
Gebreyesus ST, Muneer G, Huang CC, Siyal AA, Anand M, Chen YJ, Tu HL. Recent advances in microfluidics for single-cell functional proteomics. LAB ON A CHIP 2023; 23:1726-1751. [PMID: 36811978 DOI: 10.1039/d2lc01096h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Single-cell proteomics (SCP) reveals phenotypic heterogeneity by profiling individual cells, their biological states and functional outcomes upon signaling activation that can hardly be probed via other omics characterizations. This has become appealing to researchers as it enables an overall more holistic view of biological details underlying cellular processes, disease onset and progression, as well as facilitates unique biomarker identification from individual cells. Microfluidic-based strategies have become methods of choice for single-cell analysis because they allow facile assay integrations, such as cell sorting, manipulation, and content analysis. Notably, they have been serving as an enabling technology to improve the sensitivity, robustness, and reproducibility of recently developed SCP methods. Critical roles of microfluidics technologies are expected to further expand rapidly in advancing the next phase of SCP analysis to reveal more biological and clinical insights. In this review, we will capture the excitement of the recent achievements of microfluidics methods for both targeted and global SCP, including efforts to enhance the proteomic coverage, minimize sample loss, and increase multiplexity and throughput. Furthermore, we will discuss the advantages, challenges, applications, and future prospects of SCP.
Collapse
Affiliation(s)
- Sofani Tafesse Gebreyesus
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Gul Muneer
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | | | - Asad Ali Siyal
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
| | - Mihir Anand
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
| | - Hsiung-Lin Tu
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
| |
Collapse
|
49
|
Shijo S, Tanaka D, Sekiguchi T, Ishihara JI, Takahashi H, Kobayashi M, Shoji S. Dielectrophoresis-Based Selective Droplet Extraction Microfluidic Device for Single-Cell Analysis. MICROMACHINES 2023; 14:706. [PMID: 36985113 PMCID: PMC10058699 DOI: 10.3390/mi14030706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/18/2023] [Accepted: 03/20/2023] [Indexed: 06/18/2023]
Abstract
We developed a microfluidic device that enables selective droplet extraction from multiple droplet-trapping pockets based on dielectrophoresis. The device consists of a main microchannel, five droplet-trapping pockets with side channels, and drive electrode pairs appropriately located around the trapping pockets. Agarose droplets capable of encapsulating biological samples were successfully trapped in the trapping pockets due to the difference in flow resistance between the main and side channels. Target droplets were selectively extracted from the pockets by the dielectrophoretic force generated between the electrodes under an applied voltage of 500 V. During their extraction from the trapping pockets, the droplets and their contents were exposed to an electric field for 400-800 ms. To evaluate whether the applied voltage could potentially damage the biological samples, the growth rates of Escherichia coli cells in the droplets, with and without a voltage applied, were compared. No significant difference in the growth rate was observed. The developed device enables the screening of encapsulated single cells and the selective extraction of target droplets.
Collapse
Affiliation(s)
- Seito Shijo
- Major in Nanoscience and Nanoengineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 145-0065, Japan; (M.K.)
| | - Daiki Tanaka
- Research Organization for Nano & Life Innovation, Waseda University, 513 Tsurumakicho, Shinjuku, Tokyo 162-0041, Japan
| | - Tetsushi Sekiguchi
- Research Organization for Nano & Life Innovation, Waseda University, 513 Tsurumakicho, Shinjuku, Tokyo 162-0041, Japan
| | - Jun-ichi Ishihara
- Medical Mycology Research Center, Chiba University, 181 Inohana, Chuo, Chiba 260-8673, Japan
| | - Hiroki Takahashi
- Medical Mycology Research Center, Chiba University, 181 Inohana, Chuo, Chiba 260-8673, Japan
- Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
- Plant Molecular Science Center, Chiba University, 181 Inohana, Chuo, Chiba 260-8673, Japan
| | - Masashi Kobayashi
- Major in Nanoscience and Nanoengineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 145-0065, Japan; (M.K.)
| | - Shuichi Shoji
- Major in Nanoscience and Nanoengineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 145-0065, Japan; (M.K.)
| |
Collapse
|
50
|
Payne EM, Taraji M, Murray BE, Holland-Moritz DA, Moore JC, Haddad PR, Kennedy RT. Evaluation of Analyte Transfer between Microfluidic Droplets by Mass Spectrometry. Anal Chem 2023; 95:4662-4670. [PMID: 36862378 DOI: 10.1021/acs.analchem.2c04985] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Droplet microfluidics enables high-throughput experimentation and screening by encapsulating chemical and biochemical samples in aqueous droplets segmented by an immiscible fluid. In such experiments, it is critical that each droplet remains chemically distinct. A common approach is to use fluorinated oils with surfactants to stabilize droplets. However, some small molecules have been observed to transport between droplets under these conditions. Attempts to study and mitigate this effect have relied on evaluating crosstalk using fluorescent molecules, which inherently limits the analyte scope and conclusions drawn about the mechanism of the effect. In this work, transport of low molecular weight compounds between droplets was investigated using electrospray ionization mass spectrometry (ESI-MS) for measurement. The use of ESI-MS significantly expands the scope of analytes that can be tested. We tested 36 structurally diverse analytes that were found to exhibit crosstalk ranging from negligible to complete transfer using HFE 7500 as the carrier fluid and 008-fluorosurfactant as a surfactant. Using this data set, we developed a predictive tool showing that high log P and log D values correlate with high crosstalk, and high polar surface area and log S correlate with low crosstalk. We then investigated several carrier fluids, surfactants, and flow conditions. It was discovered that transport is strongly dependent on all of these factors and that experimental design and surfactant tailoring can reduce carryover. We present evidence for mixed crosstalk mechanisms including both micellar and oil partitioning transfer. By understanding the driving mechanisms, surfactant and oil compositions can be designed to better reduce chemical transport for screening workflows.
Collapse
Affiliation(s)
- Emory M Payne
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48103, United States
| | - Maryam Taraji
- The Australian Wine Research Institute, Adelaide, South Australia 5064, Australia.,Metabolomics Australia, Adelaide, South Australia 5064, Australia.,School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7005, Australia
| | - Bridget E Murray
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48103, United States
| | - Daniel A Holland-Moritz
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jeffrey C Moore
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Paul R Haddad
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7005, Australia
| | - Robert T Kennedy
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48103, United States
| |
Collapse
|